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Abstract Background The plant hormone auxin plays a crucial role in regulating important functions in strawberry fruit development. Although a few studies have described the complex auxin biosynthetic and signaling pathway in wild diploid strawberry (Fragaria vesca), the molecular mechanisms underlying auxin biosynthesis and crosstalk in octoploid strawberry fruit development are not fully characterized. To address this knowledge gap, comprehensive transcriptomic analyses were conducted at different stages of fruit development and compared between the achene and receptacle to identify developmentally regulated auxin biosynthetic genes and transcription factors during the fruit ripening process. Similar to wild diploid strawberry, octoploid strawberry accumulates high levels of auxin in achene compared to receptacle. Results Genes involved in auxin biosynthesis and conjugation, such as Tryptophan Aminotransferase of Arabidopsis (TAAs), YUCCA (YUCs), and Gretchen Hagen 3 (GH3s), were found to be primarily expressed in the achene, with low expression in the receptacle. Interestingly, several genes involved in auxin transport and signaling like Pin-Formed (PINs), Auxin/Indole-3-Acetic Acid Proteins (Aux/IAAs), Transport Inhibitor Response 1 / Auxin-Signaling F-Box (TIR/AFBs) and Auxin Response Factor (ARFs) were more abundantly expressed in the receptacle. Moreover, by examining DEGs and their transcriptional profiles across all six developmental stages, we identified key auxin-related genes co-clustered with transcription factors from the NAM-ATAF1,2-CUC2/ WRKYGQK motif (NAC/WYKY), Heat Shock Transcription Factor and Heat Shock Proteins (HSF/HSP), APETALA2/Ethylene Responsive Factor (AP2/ERF) and MYB transcription factor groups. Conclusions These results elucidate the complex regulatory network of auxin biosynthesis and its intricate crosstalk within the achene and receptacle, enriching our understanding of fruit development in octoploid strawberries.

Several Neopestalotiopsis spp. have been reported to affect strawberry worldwide. Here, we sequenced two isolates of Neopestalotiopsis 19-02 (highly virulent) and 13-481 (moderately virulent) recovered from commercial strawberry fields in Florida and generated chromosome-scale assemblies using the Oxford Nanopore Technologies and Illumina platforms. Each genome assembly for 19-02 and 13-481 contained putative telomere sequences at the 5′ and 3′ ends. By analyzing the collinearity of the two newly assembled genomes and verifying the conserved telomere sequence at the end of each chromosome, we confirmed that the genome of Neopestalotiopsis spp. consists of seven basic chromosomes. Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis showed 98.5% of conserved core genes for both genome assemblies, 19-02 and 13-481. Phylogenetic analysis with internal transcribed spacer, beta-tubulin, and translation elongation factor regions obtained from the assemblies 19-02 and 13-481 demonstrated that the highly virulent isolate 19-02 is phylogenetically distinct from moderate virulent N. rosae 13-481. Comparative genome analysis of the high-quality reference genome assemblies provided in this study will facilitate the identification of genomic regions responsible for the different virulence of the Neopestalotiopsis pathogen to strawberry. [Figure: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2024.

Developing new strawberry varieties with high level of disease resistance and superior fruit quality is critical for strawberry production. Despite the complexity of the octoploid strawberry genome, recent advances in genomics and DNA sequencing technologies have allowed us to identify causal sequence variants associated with specific phenotypes. These have enabled the development of new and improved DNA markers for integration in marker-assisted breeding (MAB) efforts. The use of MAB has significantly improved the efficiency of stacking loci responsible for disease resistance and fruit quality characteristics. The “Strawberry DNA Testing Handbook” is currently accessible in the Genome Database for Rosaceae and has been an essential resource for the national and international strawberry research community. Based on the information provided in the handbook, the UF strawberry breeding program implemented seedling selection from 2021 to 2023, retaining 25.3%, 19.2%, and 37.9% of seedlings for further evaluation in each respective year. In this report, we provide updates on DNA markers associated with disease resistance and fruit quality traits. Additionally, we demonstrate the practical implementation of these markers in high-throughput marker-assisted selection and their potential to enhance strawberry breeding.

Macrophomina phaseolina, the causal agent of charcoal rot, is one of the most destructive soil-borne pathogens that affect the global strawberry industry. Resistant cultivars are critical for ensuring the profitability of strawberry production without the protection historically provided by methyl bromide. Previously, three loci, namely, FaRMp1, FaRMp2, and FaRMp3, associated with quantitative resistance to Macrophomina phaseolina have been identified and validated across diverse populations and environments. Among those, the locus with the largest effect, FaRMp3, was initially detected in crosses with an exotic Fragaria ×ananassa selection. We introgressed the favorable FaRMp3 allele into elite germplasm in the University of Florida strawberry breeding program already segregating for FaRMp1 and FaRMp2 and confirmed its phenotypic effects across various genetic backgrounds. Subsequently, we developed a high-throughput genotyping assay to facilitate the transfer and selection of FaRMp3 in breeding populations via marker-assisted selection. Given that three quantitative trait loci (QTL) contribute to partial resistance to Macrophomina phaseolina, stacking them within a single genotype presents a potential strategy for enhancing resistance. We screened 564 individuals that segregate for favorable alleles at all three QTL to assess their effects singly and in combination across multiple genetic backgrounds and production seasons. Inoculated field trials revealed that the three QTL cumulatively enhanced resistance levels, and that two-way QTL combinations including FaRMp3 provide increased protection against the pathogen. Pyramiding all three loci achieved the strongest resistance and could provide substantial economic value to the strawberry industry.

The cultivated strawberry, Fragaria ×ananassa, is a recently domesticated fruit species of economic interest worldwide. As such, there is significant interest in continuous varietal improvement. Genomics-assisted improvement, including the use of DNA markers and genomic selection have facilitated significant improvements of numerous key traits during strawberry breeding. CRISPR/Cas-mediated genome editing allows targeted mutations and precision nucleotide substitutions in the target genome, revolutionizing functional genomics and crop improvement. Genome editing is beginning to gain traction in the more challenging polyploid crops, including allo-octoploid strawberry. The release of high-quality reference genomes and comprehensive subgenome-specific genotyping and gene expression profiling data in octoploid strawberry will lead to a surge in trait discovery and modification by using CRISPR/Cas. Genome editing has already been successfully applied for modification of several strawberry genes, including anthocyanin content, fruit firmness and tolerance to post-harvest disease. However, reports on many other important breeding characteristics associated with fruit quality and production are still lacking, indicating a need for streamlined genome editing approaches and tools in Fragaria ×ananassa. In this review, we present an overview of the latest advancements in knowledge and breeding efforts involving CRISPR/Cas genome editing for the enhancement of strawberry varieties. Furthermore, we explore potential applications of this technology for improving other Rosaceous plant species.

IntroductionThe strawberry industry in South Korea has witnessed a significant 65% growth over the past decade, surpassing other fruits and vegetables in production value. While sweetness and acidity are well-recognized flavor determinants, the role of volatile organic compounds (VOCs) in defining the desirable flavor profiles of strawberries is also crucial. However, existing research has predominantly concentrated on a limited range of commercial cultivars, neglecting the broader spectrum of strawberry varieties.MethodsThis study embarked on developing a comprehensive VOC database for a diverse array of strawberry cultivars sourced both domestically and internationally. A total of 61 different strawberry cultivars from Korea (45), the USA (7), Japan (8), and France (1) were analyzed for their VOC content using Tenax TA Thermo Desorption tubes and Gas Chromatography-Mass Spectrometry (GC-MS). In addition to VOC profiling, heritability was assessed using one-way ANOVA to compare means among multiple groups, providing insights into the genetic basis of flavor differences.Results and discussionThe analysis identified 122 compounds categorized into esters, alcohols, terpenes, and lactones, with esters constituting the majority (46.5%) of total VOCs in Korean cultivars. ‘Arihyang’, ‘Sunnyberry’, and ‘Kingsberry’ exhibited the highest diversity of VOCs detected (97 types), whereas ‘Seolhong’ showed the highest overall concentration (57.5mg·kg-1 FW). Compared to the USA cultivars, which were abundant in γ-decalactone (a peach-like fruity aroma), most domestic cultivars lacked this compound. Notably, ‘Misohyang’ displayed a high γ-decalactone content, highlighting its potential as breeding germplasm to improve flavor in Korean strawberries. The findings underscore the importance of a comprehensive VOC analysis across different strawberry cultivars to understand flavor composition. The significant variation in VOC content among the cultivars examined opens avenues for targeted breeding strategies. By leveraging the distinct VOC profiles, particularly the presence of γ-decalactone, breeders can develop new strawberry varieties with enhanced flavor profiles, catering to consumer preferences for both domestic and international markets.

Abstract Background The cultivated strawberry (Fragaria × ananassa Duch.) is one of the most economically important horticultural crops worldwide. Botrytis fruit rot (BFR) caused by the necrotrophic fungal pathogen Botrytis cinerea is the most devasting disease of cultivated strawberries. Most commercially grown strawberry varieties are susceptible to BFR, and controlling BFR relies on repeated applications of various fungicides. Despite extensive efforts, breeding for BFR resistance has been unsuccessful, primarily due to lack of information regarding the mechanisms of disease resistance and genetic resources available in strawberry. Results Using a reverse genetics approach, we identified candidate genes associated with BFR resistance and screened Arabidopsis mutants using strawberry isolates of B. cinerea. Among the five Arabidopsis T-DNA knockout lines tested, the mutant line with AtWRKY53 showed the greatest reduction in disease symptoms of BFR against the pathogen. Two genes, FaWRKY29 and FaWRKY64, were identified as orthologs in the latest octoploid strawberry genome, ‘Florida Brilliance’. We performed RNAi-mediated transient assay and found that the disease frequencies were significantly decreased in both FaWRKY29- and FaWRKY64-RNAi fruits of the strawberry cultivar, ‘Florida Brilliance’. Furthermore, our transcriptomic data analysis revealed significant regulation of genes associated with ABA and JA signaling, plant cell wall composition, and ROS in FaWRKY29 or FaWRKY64 knockdown strawberry fruits in response to the pathogen. Conclusion Our study uncovered the foundational role of WRKY transcription factor genes, FaWRKY29 and FaWRKY64, in conferring resistance against B. cinerea. The discovery of susceptibility genes involved in BFR presents significant potential for developing resistance breeding strategies in cultivated strawberries, potentially leveraging CRISPR-based gene editing techniques.

Abstract Phytophthora crown rot (PhCR) caused by Phytophthora cactorum is one of the most damaging diseases of strawberry worldwide. Mefenoxam is one of the major fungicides currently used to manage PhCR. However, the emergence and spread of resistant isolates have made controlling the pathogen in the field problematic. In the present study, using whole genome sequencing analysis, mutations associated with mefenoxam-resistant isolates were identified in six different genomic regions of P. cactorum. The 95.54% reads from a sensitive isolate pool and 95.65% from a resistant isolate pool were mapped to the reference genome of P. cactorum P414. Four point mutations were in coding regions while the other two were in noncoding regions. The genes harboring mutations were functionally unknown. All mutations present in resistant isolates were confirmed by sanger sequencing of PCR products. For the rapid diagnostic assay, SNP-based high-resolution melting (HRM) markers were developed to differentiate mefenoxam-resistant P. cactorum from sensitive isolates. The HRM markers R3-1F/R3-1R and R2-1F/R2-1R were suitable to differentiate both sensitive and resistant profiles using clean and crude DNA extraction. None of the mutations associated with mefenoxam resistance found in this study were in the RNA polymerase subunit genes, the hypothesized target of this compound in oomycetes. Our findings may contribute to a better understanding of the mechanisms of resistance of mefenoxam in oomycetes since serves as a foundation to validate the candidate genes as well as contribute to the monitoring of P. cactorum populations for the sustainable use of this product.

Improving flavor can be an important goal of strawberry through breeding that is enhanced through the accurate identification and quantification of flavor compounds. Herein, a targeted metabolomics strategy was developed using liquid–liquid extraction, an in-house standard database, and GC–MS/MS analysis. The database consisted of key food odorants (KFOs), artificial flavor compounds (AFCs) and volatiles. A total of 131 flavor compounds were accurately identified in Medallion® ‘FL 16.30-128′ strawberry. Importantly, ethyl vanillin was identified for the first time in natural food. Multiple techniques, including GC–MS, GC–MS/MS and UPLC-MS/MS were applied to ensure the identification. The ethyl vanillin in the Medallion® samples were determined in a range of concentrations from 0.070 ± 0.0006 µg/kg to 0.1372 ± 0.0014 µg/kg by using stable isotope dilution analysis. The identification of ethyl vanillin in strawberry implys the future commercial use a natural flavor compound and the potential to identify genes and proteins associated with its biosynthesis.

Corynespora cassiicola (Cc) is a genetically diverse ascomycete found worldwide in tropical and subtropical regions. Cc causes necrotrophic diseases in several plant species, including important crops such as rubber tree, tomato, cotton, and cucumber. Evidence suggests the involvement of one or more Cc host-specific toxins in disease progression. Management of Cc crop diseases is based mainly on pesticide sprays. However, the pathogen’s development of resistance to commonly used fungicides is documented. Resistance breeding is an attractive alternative or supplement to chemical control of Cc crop diseases, but research on this topic is very limited. This review describes the current plant resistance breeding efforts towards Cc resistance and discusses the potential influence of host-specific toxins (HSTs) on such efforts. Although some reports of host resistance exist in a few crops, resistant germplasm and knowledge about resistance mechanisms are limited. Some studies have suggested the involvement of HSTs in disease development, including the upregulation of resistance-related proteins in susceptible reactions and the recessive nature of resistance. In light of this, host resistance may not be achieved through commonly used dominant R-genes.

Our study was carried out to determine the control efficacy of sodium hypochlorite (NaOCl) for violet root rot caused by Helicobasidium mompa in apple. The experiment was conducted in the farm located at Chungbuk province in South Korea from 2014 to 2016. When infected apple trees were treated at least two or three times with 31.25 and 62.5 ml/l available chlorine content in NaOCl, it greatly increased the rooting of rootstock, and restored the tree crown density by 44.4–60.5%. In addition, the number of commercial fruit setting was increased by 54.3–64.5%, and the total starch content in shoots was significantly higher than other non-treated apple trees. However, the untreated disease control and thiophanate-methyl WP treated trees showed the symptom of dieback. Therefore, our results indicate that the drenching treatment of NaOCl with 31.25–62.5 ml/l available chlorine content more than two times from late fall to early spring could effectively control the violet root rot and recover tree vigor up to 60%.

Sheath blight is a serious rice disease worldwide, and genes involved in resistance remain unclear. In the present study, a virulent field isolate of Rhizoctonia solani was used to inoculate detached leaves of a sheath blight-resistant rice cultivar, Jasmine 85; a suppression subtractive cDNA library was constructed using RNA isolated 16 h postinoculation (hpi); and differentially expressed genes were identified from the cDNA library. A total of 159 uniquely expressed sequence tags were identified, including 105 from rice with enrichment in categories related to cellular response, molecular signaling, and host defense. Coupled with gene expression studies by DNA microarray, 27 highly induced genes involved in signal transduction and defense responses were identified within 16 hpi. Three members of the ATP-binding cassette (ABC) transporter gene family (OsABC1, OsABC9, and OsABC12) encoding pleiotropic drug resistance-like ABC transporters were mapped to different sheath blight resistance quantitative trait loci (QTLs), and their differential expressions were validated. Three high-resolution melting (HRM) markers were developed from these ABC gene family members to distinguish alleles between sheath blight-susceptible cultivar Lemont and resistant cultivar Jasmine 85. Association of sheath blight resistance to these HRM markers was examined in 77 recombinant inbred lines derived from the cross between Jasmine 85 and Lemont. The OsABC9 gene located in a major sheath blight resistance QTL qShB9-2 showed a major contribution to sheath blight resistance. These results are useful for marker-assisted selection and functional validation of the ABC genes in sheath blight disease resistance. [Figure: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2022.

Somaclonal variation is a breeding method utilizing natural genetic variation induced by a tissue culture process instead of by hybridization. This offers an alternative to mutation breeding for the introduction of new genetic variations in existing strawberry varieties. The main purpose of this new 5-page publication of the UF/IFAS Horticultural Sciences Department is to share the potential of this technique with plant breeders in the public and private industries. The secondary purpose is to educate the industry and the public on the scientific background of somaclonal variation. Written by Cheol-Min Yoo, Cheryl Dalid, Catalina Moyer, Vance Whitaker, and Seonghee Lee. https://edis.ifas.ufl.edu/hs1448

Phytophthora crown rot (PhCR) caused by Phytophthora cactorum is one of the most damaging soilborne diseases of strawberry in the United States and worldwide. Limitations on fumigants such as methyl bromide have led to deterioration in the control of P. cactorum in recent years. The development of resistant varieties is a critical component of the strategy for combatting this soilborne disease. Here, we review the biology of the pathogen, molecular mechanisms of infection, and management of PhCR in strawberry. Recent genomics advances in octoploid strawberry breeding have been able to gain a deeper insight into the genetic architecture of resistance to PhCR and identified the genetic resistance sources for the improvement of strawberry varieties against the pathogen. Quantitative trait loci (QTL) associated with PhCR resistance have been identified and introgressed for breeding of PhCR resistance in cultivated octoploid strawberry (F. × ananassa). Further characterizing candidate genes and mechanisms of resistance could facilitate incorporating the resistance genes into commercial varieties through genomics-assisted breeding, respectively. In this review, we address important recent advances and progress for genomics-assisted breeding for the resistance to PhCR and the potential use of CRISPR gene editing in cultivated strawberry.

Many plant-encoded E3 ligases are known to be involved in plant defense. Here, we report a novel role of E3 ligase SALT- AND DROUGHT-INDUCED RING FINGER1 (SDIR1) in plant immunity. Even though SDIR1 is reasonably well-characterized, its role in biotic stress response is not known. The silencing of SDIR1 in Nicotiana benthamiana reduced the multiplication of the virulent bacterial pathogen Pseudomonas syringae pv. tabaci. The Arabidopsis sdir1 mutant is resistant to virulent pathogens, whereas SDIR1 overexpression lines are susceptible to both host and nonhost hemibiotrophic bacterial pathogens. However, sdir1 mutant and SDIR1 overexpression lines showed hypersusceptibility and resistance, respectively, against the necrotrophic pathogen Erwinia carotovora. The mutant of SDIR1 target protein, i.e., SDIR-interacting protein 1 (SDIR1P1), also showed resistance to host and nonhost pathogens. In SDIR1 overexpression plants, transcripts of NAC transcription factors were less accumulated and the levels of jasmonic acid (JA) and abscisic acid were increased. In the sdir1 mutant, JA signaling genes JAZ7 and JAZ8 were downregulated. These data suggest that SDIR1 is a susceptibility factor and its activation or overexpression enhances disease caused by P. syringae pv. tomato DC3000 in Arabidopsis. Our results show a novel role of SDIR1 in modulating plant defense gene expression and plant immunity.

FaRCa1 is a major locus conferring resistance to anthracnose fruit rot (AFR) caused by Colletotrichum acutatum, an important pathogen of strawberry (Fragaria ×ananassa). The objective of this study was to characterize the effects of FaRCa1 on anthracnose root necrosis (ARN) via root inoculations and DNA marker characterization of the locus. A subgenome-specific high-resolution melting (HRM) marker for an insertion/deletion (InDel) near FaRCa1 was designed using the ‘Camarosa’ octoploid reference genome. The marker was used to genotype cultivars and advanced selections studied in two seasons. A root disease screening method was developed in which roots were cut and dipped in a spore suspension before planting, using a mixture of three local isolates of the C. acutatum species complex. ARN was indirectly scored by calculating image-based leaf area differences among inoculated and noninoculated plants. The allele of FaRCa1 conferring resistance to AFR also conferred a significant reduction in ARN. Thus, a robust and easily scored DNA test is now available to breeders for selecting for resistance to both the fruit and root forms of strawberry anthracnose.

Nonhost disease resistance is the most common type of plant defense mechanism against potential pathogens. In the present study, the metabolic enzyme formate dehydrogenase 1 (FDH1) was identified to associate with nonhost disease resistance in Nicotiana benthamiana and Arabidopsis thaliana. In Arabidopsis, AtFDH1 was highly upregulated in response to both host and nonhost bacterial pathogens. The Atfdh1 mutants were compromised in nonhost resistance, basal resistance, and gene-for-gene resistance. The expression patterns of salicylic acid (SA) and jasmonic acid (JA) marker genes after pathogen infections in Atfdh1 mutant indicated that both SA and JA are involved in the FDH1-mediated plant defense response to both host and nonhost bacterial pathogens. Previous studies reported that FDH1 localizes to mitochondria, or both mitochondria and chloroplasts. Our results showed that the AtFDH1 mainly localized to mitochondria, and the expression level of FDH1 was drastically increased upon infection with host or nonhost pathogens. Furthermore, we identified the potential co-localization of mitochondria expressing FDH1 with chloroplasts after the infection with nonhost pathogens in Arabidopsis. This finding suggests the possible role of FDH1 in mitochondria and chloroplasts during defense responses against bacterial pathogens in plants.

Colletotrichum crown rot (CCR) caused by Colletotrichum gloeosporioides is a serious threat to the cultivated strawberry (Fragaria × ananassa). Our previous study reported that a major locus, FaRCg1, increases resistance. However, the genomic structure of FaRCg1 and potential candidate genes associated with the resistance remained unknown. Here, we performed comparative transcriptome analyses of resistant ‘Florida Elyana’ and susceptible ‘Strawberry Festival’ after infection and identified candidate genes potentially involved in resistance. In ‘Florida Elyana’, 6,099 genes were differentially expressed in response to C. gloeosporioides. Gene ontology analysis showed that the most upregulated genes were functionally associated with signaling pathways of plant defense responses. Three genes in the genomic region of FaRCg1 were highly upregulated: a von Willebrand Factor A domain-containing protein, a subtilisin-like protease, and a TIFY 11A-like protein. Subgenome-specific markers developed for the candidate genes were tested with a diverse panel of 219 accessions from University of Florida and North Carolina State University breeding programs. Significant and positive associations were found between the high-resolution melting (HRM) marker genotypes and CCR phenotypes. These newly developed subgenome-specific functional markers for FaRCg1 can facilitate development of resistant varieties through marker-assisted selection.

Strawberries produce numerous volatile compounds that contribute to the unique flavors of fruits. Among the many volatiles, γ-decalactone (γ-D) has the greatest contribution to the characteristic fruity aroma in strawberry fruit. The presence or absence of γ-D is controlled by a single locus, FaFAD1. However, this locus has not yet been systematically characterized in the octoploid strawberry genome. It has also been reported that the volatile content greatly varies among the strawberry varieties possessing FaFAD1, suggesting that another genetic factor could be responsible for the different levels of γ-D in fruit. In this study, we explored the genomic structure of FaFAD1 and determined the allele dosage of FaFAD1 that regulates variations of γ-D production in cultivated octoploid strawberry. The genome-wide association studies confirmed the major locus FaFAD1 that regulates the γ-D production in cultivated strawberry. With the hybrid capture-based next-generation sequencing analysis, a major presence–absence variation of FaFAD1 was discovered among γ-D producers and non-producers. To explore the genomic structure of FaFAD1 in the octoploid strawberry, three bacterial artificial chromosome (BAC) libraries were developed. A deletion of 8,262 bp was consistently found in the FaFAD1 region of γ-D non-producing varieties. With the newly developed InDel-based codominant marker genotyping, along with γ-D metabolite profiling data, we revealed the impact of gene dosage effect for the production of γ-D in the octoploid strawberry varieties. Altogether, this study provides systematic information of the prominent role of FaFAD1 presence and absence polymorphism in producing γ-D and proposes that both alleles of FaFAD1 are required to produce the highest content of fruity aroma in strawberry fruit.

The cultivated strawberry (Fragaria × ananassa) is an economically important fruit crop that is intensively bred for improved sensory qualities. The diversity of fruit flavors and aromas in strawberry results mainly from the interactions of sugars, acids, and volatile organic compounds (VOCs) that are derived from diverse biochemical pathways influenced by the expression of many genes. This study integrates multiomic analyses to identify QTL and candidate genes for multiple aroma compounds in a complex strawberry breeding population. Novel fruit volatile QTL was discovered for methyl anthranilate, methyl 2-hexenoate, methyl 2-methylbutyrate, mesifurane, and a shared QTL on Chr 3 was found for nine monoterpene and sesquiterpene compounds, including linalool, 3-carene, β-phellandrene, α-limonene, linalool oxide, nerolidol, α-caryophellene, α-farnesene, and β-farnesene. Fruit transcriptomes from a subset of 64 individuals were used to support candidate gene identification. For methyl esters including the grape-like methyl anthranilate, a novel ANTHANILIC ACID METHYL TRANSFERASE–like gene was identified. Two mesifurane QTL correspond with the known biosynthesis gene O-METHYL TRANSFERASE 1 and a novel FURANEOL GLUCOSYLTRANSFERASE. The shared terpene QTL contains multiple fruit-expressed terpenoid pathway-related genes including NEROLIDOL SYNTHASE 1 (FanNES1). The abundance of linalool and other monoterpenes is partially governed by a co-segregating expression-QTL (eQTL) for FanNES1 transcript variation, and there is additional evidence for quantitative effects from other terpenoid-pathway genes in this narrow genomic region. These QTLs present new opportunities in breeding for improved flavor in commercial strawberry.

Octoploid strawberry (Fragaria ×ananassa) is a valuable specialty crop, but profitable production and availability are threatened by many pathogens. Efforts to identify and introgress useful disease resistance genes (R-genes) in breeding programs are complicated by strawberry’s complex octoploid genome. Recently-developed resources in strawberry, including a complete octoploid reference genome and high-resolution octoploid genotyping, enable new analyses in strawberry disease resistance genetics. This study characterizes the complete R-gene collection in the genomes of commercial octoploid strawberry and two diploid ancestral relatives, and introduces several new technological and data resources for strawberry disease resistance research. These include octoploid R-gene transcription profiling, dN/dS analysis, expression quantitative trait loci (eQTL) analysis and RenSeq analysis in cultivars. Octoploid fruit eQTL were identified for 76 putative R-genes. R-genes from the ancestral diploids Fragaria vesca and Fragaria iinumae were compared, revealing differential inheritance and retention of various octoploid R-gene subtypes. The mode and magnitude of natural selection of individual F. ×ananassa R-genes was also determined via dN/dS analysis. R-gene sequencing using enriched libraries (RenSeq) has been used recently for R-gene discovery in many crops, however this technique somewhat relies upon a priori knowledge of desired sequences. An octoploid strawberry capture-probe panel, derived from the results of this study, is validated in a RenSeq experiment and is presented for community use. These results give unprecedented insight into crop disease resistance genetics, and represent an advance toward exploiting variation for strawberry cultivar improvement.

Octoploid strawberry (Fragaria ×ananassa) is a major specialty crop under intense annual selection for traits relating to plant vigor and fruit quality. Most functional validation experiments rely on transgenic or transient gene expression assays in the mature receptacle. These findings are not typically translatable to breeding without identifying a natural genetic source of transcript level variation, and developing reliable markers for selection in octoploids. Expression QTL (eQTL) analysis is a genetic/transcriptomic association approach for identifying sequence variants predicting differential expression. This eQTL study analyzed a wide array of mature receptacle-expressed genes, encompassing the majority of total mature receptacle transcript accumulation and almost all strawberry genes described in the literature. These results identified segregating genetic variants associated with the differential expression of hundreds of strawberry genes, many with known interest to breeders. Several of these eQTL pertain to published genes whose expression levels have been demonstrated to influence mature receptacle phenotypes. Many include key genes of the phenylpropanoid pathway, vitamin C, carotenoid, pectin, and receptacle carbohydrate/sugar metabolism. These subgenome-specific genetic markers may allow breeders to select for desired ranges of target gene expression. These results may also guide basic research efforts and facilitate the identification of causal genes underlying trait QTL.

Abstract Plant defense responses at stomata and apoplast are the most important early events during plant-bacteria interactions. The key components for the signaling of stomatal defense and nonhost resistance have not been fully characterized. Here we report the newly identified small GTPase, Nucleolar GTP-binding protein 1 (NOG1), functions for plant immunity against bacterial pathogens. Virus-induced gene silencing of NOG1 compromised nonhost resistance in N. benthamiana and tomato. Comparative genomic analysis showed that two NOG1 copies are present in all known plant species: NOG1-1 and NOG1-2. Gene downregulation and overexpression studies of NOG1-1 and NOG1-2 in Arabidopsis revealed the novel function of these genes in nonhost resistance and stomatal defense against bacterial pathogens, respectively. Specially, NOG1-2 regulates guard cell signaling in response to biotic and abiotic stimuli through jasmonic acid (JA)- and abscisic acid (ABA)-mediated pathways. The results here provide valuable information on the new functional role of small GTPase, NOG1, in guard cell signaling and early plant defense in response to bacterial pathogens.

Recently, new plant-breeding technology such as CRISPR gene editing has provided the potential to substantially improve crop breeding in agriculture. Considerable efforts have been devoted to apply this gene-editing technology in modern agriculture to increase crop yields and improve the quality of food ingredients, especially by many of the major agronomic seed-producing companies. In this new 4-page article, we outline the recent research updates and regulations on gene editing in crop improvement. Written by Sadikshya Sharma, Heqiang Huo, and Seonghee Lee and published by the UF/IFAS Horticultural Sciences Department. https://edis.ifas.ufl.edu/hs1334

Because cultivated strawberries are genetically complex, conventional breeding of strawberry can be difficult. Therefore, gene editing can be useful when developing strawberry varieties. This 3-page document discusses CRISPR gene editing in strawberry. Written by Seonghee Lee, Cheolmin Yoo, Kevin Folta, and Vance M. Whitaker and published by the UF/IFAS Horticultural Sciences Department, February 2018. http://edis.ifas.ufl.edu/hs1315

Are Florida strawberries genetically engineered? The answer is no. No genetically engineered strawberry has been commercialized anywhere in the world. The UF/IFAS strawberry breeding program has been developing strawberry varieties for nearly 70 years, but these varieties are developed using a conventional breeding process of crossing and selection. This 4-page fact sheet describes that process in greater detail. Written by Seonghee Lee, Young-Hee Noh, Sujeet Verma, and Vance M. Whitaker, and published by the Horticultural Sciences Department, November 2016. HS1287/HS1287: DNA, Technology, and Florida Strawberries (ufl.edu) Also see the UF/IFAS press release (12/14): UF/IFAS scientists: Commercially grown strawberries are not genetically engineered

Plant breeding for disease resistance is crucial to sustain global crop production. For decades, plant breeders and researchers have extensively used host plant resistance genes (R-genes) to develop disease resistant cultivars. However, the general instability of R-genes in crop cultivars when challenged with diverse pathogen populations emphasizes the need for more stable means of resistance. Alternatively, nonhost resistance is recognized as the most durable, broad-spectrum form of resistance against the majority of potential pathogens in plants and has gained great attention as an alternative target for managing resistance. While transgenic approaches have been utilized to transfer nonhost resistance to host species, conventional breeding applications have been more elusive. Nevertheless, avenues for discovery and deployment of genetic loci for nonhost resistance via hybridization are increasingly abundant, particularly when transferring genes among closely related species. In this mini review, we discuss current and developing applications of nonhost resistance for crop improvement with a focus on the overlap between host and nonhost mechanisms and the potential impacts of new technology.

Plant defense responses at stomata and apoplast are the most important early events during plant–bacteria interactions. The key components of stomatal defense responses have not been fully characterized. A GTPase encoding gene, NOG1-2, which is required for stomatal innate immunity against bacterial pathogens, was recently identified. Functional studies in Arabidopsis revealed that NOG1-2 regulates guard cell signaling in response to biotic and abiotic stimulus through jasmonic acid (JA)- and abscisic acid (ABA)-mediated pathways. Interestingly, in this study, Jasmonate-ZIM-domain protein 9 (JAZ9) was identified to interact with NOG1-2 for the regulation of stomatal closure. Upon interaction, JAZ9 reduces GTPase activity of NOG1-2. We explored the role of NOG1-2 binding with JAZ9 for COI1-mediated JA signaling and hypothesized that its function may be closely linked to MYC2 transcription factor in the regulation of the JA-signaling cascade in stomatal defense against bacterial pathogens. Our study provides valuable information on the function of a small GTPase, NOG1-2, in guard cell signaling and early plant defense in response to bacterial pathogens.

Pseudomonas syringae is the most widespread bacterial pathogen in plants. Several strains of P. syringae produce a phytotoxin, coronatine (COR), which acts as a jasmonic acid mimic and inhibits plant defense responses and contributes to disease symptom development. In this study, we found that COR inhibits early defense responses during nonhost disease resistance. Stomatal closure induced by a nonhost pathogen, P. syringae pv. tabaci, was disrupted by COR in tomato epidermal peels. In addition, nonhost HR cell death triggered by P. syringae pv. tabaci on tomato was remarkably delayed when COR was supplemented along with P. syringae pv. tabaci inoculation. Using isochorismate synthase (ICS)-silenced tomato plants and transcript profiles of genes in SA- and JA-related defense pathways, we show that COR suppresses SA-mediated defense during nonhost resistance.

Heterotrimeric G-proteins have been proposed to be involved in many aspects of plant disease resistance but their precise role in mediating nonhost disease resistance is not well understood. We evaluated the roles of specific subunits of heterotrimeric G-proteins using knock-out mutants of Arabidopsis Gα, Gβ and Gγ subunits in response to host and nonhost Pseudomonas pathogens. Plants lacking functional Gα, Gβ and Gγ1Gγ2 proteins displayed enhanced bacterial growth and disease susceptibility in response to host and nonhost pathogens. Mutations of single Gγ subunits Gγ1, Gγ2 and Gγ3 did not alter bacterial disease resistance. Some specificity of subunit usage was observed when comparing host pathogen versus nonhost pathogen. Overexpression of both Gα and Gβ led to reduced bacterial multiplication of nonhost pathogen P. syringae pv. tabaci whereas overexpression of Gβ, but not of Gα, resulted in reduced bacterial growth of host pathogen P. syringae pv. maculicola, compared to wild-type Col-0. Moreover, the regulation of stomatal aperture by bacterial pathogens was altered in Gα and Gβ mutants but not in any of the single or double Gγ mutants. Taken together, these data substantiate the critical role of heterotrimeric G-proteins in plant innate immunity and stomatal modulation in response to P. syringae.

The Pi-ta gene in rice has been effectively used to control rice blast disease caused by Magnaporthe oryzae worldwide. Despite a number of studies that reported the Pi-ta gene in domesticated rice and wild species, little is known about how the Pi-ta gene has evolved in US weedy rice, a major weed of rice. To investigate the genome organization of the Pi-ta gene in weedy rice and its relationship to gene flow between cultivated and weedy rice in the US, we analyzed nucleotide sequence variation at the Pi-ta gene and its surrounding 2 Mb region in 156 weedy, domesticated and wild rice relatives. We found that the region at and around the Pi-ta gene shows very low genetic diversity in US weedy rice. The patterns of molecular diversity in weeds are more similar to cultivated rice (indica and aus), which have never been cultivated in the US, rather than the wild rice species, Oryza rufipogon. In addition, the resistant Pi-ta allele (Pi-ta) found in the majority of US weedy rice belongs to the weedy group strawhull awnless (SH), suggesting a single source of origin for Pi-ta. Weeds with Pi-ta were resistant to two M. oryzae races, IC17 and IB49, except for three accessions, suggesting that component(s) required for the Pi-ta mediated resistance may be missing in these accessions. Signatures of flanking sequences of the Pi-ta gene and SSR markers on chromosome 12 suggest that the susceptible pi-ta allele (pi-ta), not Pi-ta, has been introgressed from cultivated to weedy rice by out-crossing.

Macrophomina phaseolina, the causal agent of charcoal rot, is one of the most destructive soil-borne pathogens that affect the global strawberry industry. Resistant cultivars are critical for ensuring the profitability of strawberry production without the protection historically provided by methyl bromide. Previously, three loci, namely, FaRMp1, FaRMp2, and FaRMp3, associated with quantitative resistance to Macrophomina phaseolina have been identified and validated across diverse populations and environments. Among those, the locus with the largest effect, FaRMp3, was initially detected in crosses with an exotic Fragaria xananassa selection. We introgressed the favorable FaRMp3 allele into elite germplasm in the University of Florida strawberry breeding program already segregating for FaRMp1 and FaRMp2 and confirmed its phenotypic effects across various genetic backgrounds. Subsequently, we developed a high-throughput genotyping assay to facilitate the transfer and selection of FaRMp3 in breeding populations via marker-assisted selection. Given that three quantitative trait loci (QTL) contribute to partial resistance to Macrophomina phaseolina, stacking them within a single genotype presents a potential strategy for enhancing resistance. We screened 564 individuals that segregate for favorable alleles at all three QTL to assess their effects singly and in combination across multiple genetic backgrounds and production seasons. Inoculated field trials revealed that the three QTL cumulatively enhanced resistance levels, and that two-way QTL combinations including FaRMp3 provide increased protection against the pathogen. Pyramiding all three loci achieved the strongest resistance and could provide substantial economic value to the strawberry industry. [ABSTRACT FROM AUTHOR]